Thanks for the welcome wagon. I've been lurking in the depths for quite some time and finally decided to surface.
Just an update to this problem, I've been able to get the same "death everywhere" problem to kick up with the IXB/IX3 combination. I went deep into the game files and changed the availabilty dates of the upgrades so I was able to get a fully equipped type IX in early '40. Then it was off to play chicken with destroyers. I get their attention and then charge at them at flank speed, surfaced, and deck gun blazing. (NOT recommended if you plan on having a long career
) After multiple tries, the destroyer finally lands the right hit. Boom! "Watchtower is damaged, sir!" is filling up my message box as fast as it can be printed out on the screen. Check the damage diagram, click on the conning tower, and there it is, minor damage to the watchtower. (by this time, at least half of the crew has already gone up to suicide) For the sake of testing, I gave the conning tower 8000 hit points and gave the crewmen an equally ridiculous amount of hitpoints.
Didn't make a difference, when the destroyer lands the right shot, it's all over.
I'm leaning more towards the problem lying with the IX3 tower, not which sub type it's on. This was done with a fresh install of SHIII, patched, and GWX 1.03 with latest patches. So, I was able to achieve the same result, but still haven't found a fix or workaround aside from not using the IX3 tower.